Back to the "Multiple platform build/check report"

BioC experimental data: CHECK report for encoDnaseI on linux2.bioconductor.org

This page was generated on 2015-10-24 19:25:27 -0400 (Sat, 24 Oct 2015).

Package 76/257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
encoDnaseI 0.9.0
VJ Carey
Snapshot Date: 2015-10-24 10:15:05 -0400 (Sat, 24 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/encoDnaseI
Last Changed Rev: 3462 / Revision: 3473
Last Changed Date: 2015-10-13 16:20:35 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: encoDnaseI
Version: 0.9.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings encoDnaseI_0.9.0.tar.gz
StartedAt: 2015-10-24 12:07:13 -0400 (Sat, 24 Oct 2015)
EndedAt: 2015-10-24 12:12:13 -0400 (Sat, 24 Oct 2015)
EllapsedTime: 299.7 seconds
RetCode: 0
Status:  OK 
CheckDir: encoDnaseI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings encoDnaseI_0.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/encoDnaseI.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘encoDnaseI/DESCRIPTION’ ... OK
* this is package ‘encoDnaseI’ version ‘0.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘encoDnaseI’ can be installed ... [27s/29s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GGBase’ ‘GGtools’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
WRC: warning in matrix(ans, nr = 2): partial argument match of 'nr' to
  'nrow'
makeHg18track: warning in matrix(dataVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
[,hg18track-ANY-ANY-ANY: warning in matrix(dataVals(x)[kpinds], nc =
  1): partial argument match of 'nc' to 'ncol'
ALICOR: no visible binding for global variable ‘rawCD4’
ALICOR: no visible global function definition for ‘p.value’
WRC: no visible binding for global variable ‘d19’
juxtaPlot: no visible global function definition for ‘p.value’
juxtaPlot: no visible global function definition for ‘xyplot’
Undefined global functions or variables:
  d19 p.value rawCD4 xyplot
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'snpMatrix'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘SNPlocs.Hsapiens.dbSNP.20090506’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-data-experiment/meat/encoDnaseI.Rcheck/00check.log’
for details.


encoDnaseI.Rcheck/00install.out:

* installing *source* package ‘encoDnaseI’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: aggregate
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: aggregate
* DONE (encoDnaseI)

encoDnaseI.Rcheck/encoDnaseI-Ex.timings:

nameusersystemelapsed
encoDnaseI2.0590.0682.128
hg18track-class2.8870.0442.939
juxtaPlot0.0000.0000.001